I knew the rule but having re-read 12.41, I can see where confusion could be - the "Negative column modifiers for dug-in units (16.2) only benefit defending units..." sounds like it would apply to Assaults but when you read 16.2 it does point out "First Fire in assaults". The part in the assault section could have been a little clearer.
In fact, if you look at the 2nd, 3rd and 4th edition charts here:
All Charts you will see that there was never a dug in modifier for assaults so not quite sure why it was in that section of the rules.